Differential annotation of tRNA genes with anticodon CAT in bacterial genomes

We have developed three strategies to discriminate among the three types of tRNA genes with anticodon CAT (tRNA(Ile), elongator tRNA(Met) and initiator tRNA(fMet)) in bacterial genomes. With these strategies, we have classified the tRNA genes from 234 bacterial and several organellar genomes. These sequences, in an aligned or unaligned format, may be used for the identification and annotation of tRNA (CAT) genes in other genomes. The first strategy is based on the position of the problem sequences in a phenogram (a tree-like network), the second on the minimum average number of differences against the tRNA sequences of the three types and the third on the search for the highest score value against the profiles of the three types of tRNA genes. The species with the maximum number of tRNA(fMet) and tRNA(Met) was Photobacterium profundum, whereas the genome of one Escherichia coli strain presented the maximum number of tRNA(Ile) (CAT) genes. This last tRNA gene and tilS, encoding an RNA-modifying enzyme, are not essential in bacteria. The acquisition of a tRNA(Ile) (TAT) gene by Mycoplasma mobile has led to the loss of both the tRNA(Ile) (CAT) and the tilS genes. The new tRNA has appropriated the function of decoding AUA codons

Mobile genetic element proliferation and gene inactivation impact over the genome structure and metabolic capabilities of Sodalis glossinidius, the secondary endosymbiont of tsetse flies

<p>Abstract</p> <p>Background</p> <p>Genome reduction is a common evolutionary process in symbiotic and pathogenic bacteria. This process has been extensively characterized in bacterial endosymbionts of insects, where primary mutualistic bacteria represent the most extreme cases of genome reduction consequence of a massive process of gene inactivation and loss during their evolution from free-living ancestors. <it>Sodalis glossinidius</it>, the secondary endosymbiont of tsetse flies, contains one of the few complete genomes of bacteria at the very beginning of the symbiotic association, allowing to evaluate the relative impact of mobile genetic element proliferation and gene inactivation over the structure and functional capabilities of this bacterial endosymbiont during the transition to a host dependent lifestyle.</p> <p>Results</p> <p>A detailed characterization of mobile genetic elements and pseudogenes reveals a massive presence of different types of prophage elements together with five different families of IS elements that have proliferated across the genome of <it>Sodalis glossinidius </it>at different levels. In addition, a detailed survey of intergenic regions allowed the characterization of 1501 pseudogenes, a much higher number than the 972 pseudogenes described in the original annotation. Pseudogene structure reveals a minor impact of mobile genetic element proliferation in the process of gene inactivation, with most of pseudogenes originated by multiple frameshift mutations and premature stop codons. The comparison of metabolic profiles of <it>Sodalis glossinidius </it>and tsetse fly primary endosymbiont <it>Wiglesworthia glossinidia </it>based on their whole gene and pseudogene repertoires revealed a novel case of pathway inactivation, the arginine biosynthesis, in <it>Sodalis glossinidius </it>together with a possible case of metabolic complementation with <it>Wigglesworthia glossinidia </it>for thiamine biosynthesis.</p> <p>Conclusions</p> <p>The complete re-analysis of the genome sequence of <it>Sodalis glossinidius </it>reveals novel insights in the evolutionary transition from a free-living ancestor to a host-dependent lifestyle, with a massive proliferation of mobile genetic elements mainly of phage origin although with minor impact in the process of gene inactivation that is taking place in this bacterial genome. The metabolic analysis of the whole endosymbiotic consortia of tsetse flies have revealed a possible phenomenon of metabolic complementation between primary and secondary endosymbionts that can contribute to explain the co-existence of both bacterial endosymbionts in the context of the tsetse host.</p

Técnicas de ahorro de sangre en cirugía ortopédica

La cirugía ortopédica está asociada con frecuencia a la necesidad de transfusión de sangre homóloga, con los consiguientes riesgos que ello conlleva. En la actualidad se resalta la importancia de la disminución tanto de la transfusión como de la sobretransfusión en este tipo de cirugía. Dicho objetivo se puede alcanzar con el empleo de diversas técnicas de ahorro de sangre, que incluyan la potenciación del uso de sangre antóloga de métodos para disminuir el sangrado perioperatorio. La máxima eficacia para disminuir la necesidad de transfusión de sangre homóloga se deriva de la combinación de varias técnicas de ahorro, como son los programas de autotransfusión, la hipotensión controlada y el empleo de nuevos fármacos como eritropoyetina o aprotinina; todo ello sin olvidar la importancia de establecer unos criterios restrictivos, en consonancia con las directrices más actuales en este sentido, en el momento de indicar la necesidad de una transfusión sanguínea.Technique in orthopaedic surgery requires frequently transfusion of homologous blood which entails several risks. Nowadays, the importance of the decrease of both transfusion and overtransfusion has been proposed for this type of surgery. This aim can be reached by using different blood saving techniques including either the use of antologous blood or methods to minimize perioperative bleeding. The highest efficacy in order to diminish homologous blood transfusion combines several savings techniques as autotransfusion programs, controlled hypotension, and the use of new drugs such as erytropoyetin and aproinin. Restrictive criteria have to be established according to the more recent guidelines for blood transfusion

Massive presence of insertion sequences in the genome of SOPE, the primary endosymbiont of the rice weevil Sitophilus oryzae

Bacteria that establish an obligate intracellular relationship with eukaryotic hosts undergo an evolutionary genomic reductive process. Recent studies have shown an increase in the number of mobile elements in the first stage of the adaptive process towards intracellular life, although these elements are absent in ancient endosymbionts. Here, the genome of SOPE, the obligate mutualistic endosymbiont of rice weevils, was used as a model to analyze the initial events that occur after symbiotic integration. During the first phases of the SOPE genome project, four different types of insertion sequence (IS) elements, belonging to well-characterized IS families from γ-proteobacteria, were identified. In the present study, these elements, which may represent more than 20% of the complete genome, were completely characterized; their relevance as a source of gene inactivation, chromosomal rearrangements, and as participants in the genome reductive process are discussed herein. [Int Microbiol 2008; 11(1): 41-48

Massive presence of insertion sequences in the genome of SOPE, the primary endosymbiont of the rice weevil Sitophilus oryzae

Bacteria that establish an obligate intracellular relationship with eukaryotic hosts undergo an evolutionary genomic reductive process. Recent studies have shown an increase in the number of mobile elements in the first stage of the adaptive process towards intracellular life, although these elements are absent in ancient endosymbionts. Here, the genome of SOPE, the obligate mutualistic endosymbiont of rice weevils, was used as a model to analyze the initial events that occur after symbiotic integration. During the first phases of the SOPE genome project, four different types of insertion sequence (IS) elements, belonging to well-characterized IS families from γ-proteobacteria, were identified. In the present study, these elements, which may represent more than 20% of the complete genome, were completely characterized; their relevance as a source of gene inactivation, chromosomal rearrangements, and as participants in the genome reductive process are discussed herein.Gil Garcia, Rosario, [email protected] ; Belda Cuesta, Eugenio, [email protected] ; Gosalbes Soler, Maria Jose, [email protected] ; Delaye, Luis, [email protected] ; Silva Moreno, Francisco J., [email protected] ; Moya Simarro, Andres, [email protected] ; Latorre Castillo, Amparo, [email protected]

First data about the status of the Cabrera vole Iberomys cabrerae (Thomas, 1906) in Castelló and the expansion of its distribution to the south of the province of València

Se registra por primera vez en la provincia de Castelló el topillo de Cabrera Iberomys cabrerae (Thomas, 1906) en tiempos recientes, donde tan solo se contaba con registro fósil en varios yacimientos datados en el Neolítico. Además se amplía hacia el sur su distribución conocida en València. Se describe y comenta su descubrimiento en la sierra del Toro (l'Alt Palància) y en la Font de la Figuera (la Costera).This is the first recorded finding in recent times of the Cabrera vole Iberomys cabrerae (Thomas, 1906) in Castelló province, where previously only fossil records have been identified in several Neolithic sites. In addition, it's known distribution is expanded to the south of the province of València. These discoveries, made in the Sierra del Toro (l'Alt Palància) and la Font de la Figuera (la Costera), are described and commented upon.Este estudio ha sido financiado por el Servicio de Vida Silvestre de la Conselleria de Agricultura, Medio Ambiente, Cambio Climático y Desarrollo Rural de la Generalitat Valenciana

Caso clínico de anestesia

Historia clínica. Se presentó en el Hospital Clínico Veterinario de la Universidad de Murcia un perro de raza mestiza, 8 kg de peso y 5 años de edad, con una cojera en la extremidad posterior izquierda. El propietario cuenta que el animal está siendo tratado de un absceso en la almohadilla plantar, y que en los últimos días ha empezado a supurar a través de un dedo

Intelligent transport systems harmonisation assessment: use case of some Spanish intelligent transport systems services

From the 1980s, new telematic technologies have meant a great evolution in several areas. In the transportation domain, their use has implied the development and implementation of several intelligent transport systems (ITS). However, these deployments were done in an isolated way. Traffic managers, public and private organisations, stakeholders and others have implemented ITS without much perspective, that is, without providing ITS as services for end users. In the last few years, several European Union (EU) funded projects have been dealing with the development of harmonised ITS services. For example, the EasyWay Project is involving most of the European countries (EU member states and others) to deploy harmonised ITS services taking into account the European citizen as the final target. In this study, an introduction of the EasyWay project is made, including the ITS concept services and the deployment guidelines for harmonisation. In November 2012, EasyWay presented a new version of DGs, which were approved with minor editorial changes. An overview on these DGs for the ITS services is presented and two real Spanish road traffic ITS services are analysed

Seguimiento de la cubierta vegetal en la península ibérica a partir de sensores de nueva generación y su interrelación con variables climáticas

Ponencia presentada en: XIII Congreso de la Asociación Española de Teledetección celebrado en Calatayud del 23 al 26 septiembre 2009.[ES]El objetivo principal del proyecto DULCINEA ha sido el desarrollo de una metodología multi-sensor para estimar parámetros biofísicos de la cubierta vegetal. La metodología desarrollada ha proporcionado estimaciones precisas de variables biofísicas de la vegetación (FVC, LAI) que han mostrado ser adecuadas para observar las variaciones inter- e intra-anuales de la cubierta en la Península Ibérica durante un periodo de 9 años (2000-2008). Los parámetros biofísicos obtenidos han permitido evaluar la vulnerabilidad de la vegetación ante condiciones ambientales extremas a nivel de la Península Ibérica. Un paso previo ha consistido en la elaboración de mapas detallados de parámetros climáticos y tipos de cubierta dominantes en la zona. Los modelos estadísticos aplicados han evidenciado una correlación significativa entre las variables biofísicas extraídas y algunas variables meteorológicas e índices de sequía operacionales. Esta interrelación es muy dependiente del tipo de cubierta y de las características climáticas de cada región. Se han encontrado correlaciones entre las anomalías de la cobertura vegetal y el SPI especialmente significativas para el caso de las regiones más secas, con valores típicos de R2 entre 0.4 y 0.7 durante los meses de Mayo y Junio.[EN]The main objective of the DULCINEA project is to provide coherent estimates of bio-physical variables such as fractional vegetation cover (FVC) and leaf area index (LAI) at regional to global scales. One of the goals of the project is to assess the potential of derived biophysical variables in the field of drought conditions monitoring. The aim was to analyse the vulnerability of natural ecosystems against the effects of climate fluctuations like drought and extreme events in the Iberian Peninsula, from the inter-correlation between the retrieved parameters and drought indices such as the Standardized Precipitation Index (SPI). The climatic disturbances affected both the growing season and the total amount of vegetation. Strong correlations have been found between SPI and satellitederived vegetation products, which are particularly significant in semi-arid regions.Este trabajo se enmarca en el proyecto DULCINEA (CGL2005-04202) y ha contado además con el soporte del proyecto ÁRTEMIS (CGL2008-00381)

Metabolic Networks of Sodalis glossinidius: A Systems Biology Approach to Reductive Evolution

Background: Genome reduction is a common evolutionary process affecting bacterial lineages that establish symbiotic or pathogenic associations with eukaryotic hosts. Such associations yield highly reduced genomes with greatly streamlined metabolic abilities shaped by the type of ecological association with the host. Sodalis glossinidius, the secondary endosymbiont of tsetse flies, represents one of the few complete genomes available of a bacterium at the initial stages of this process. In the present study, genome reduction is studied from a systems biology perspective through the reconstruction and functional analysis of genome-scale metabolic networks of S. glossinidius. Results: The functional profile of ancestral and extant metabolic networks sheds light on the evolutionary events underlying transition to a host-dependent lifestyle. Meanwhile, reductive evolution simulations on the extant metabolic network can predict possible future evolution of S. glossinidius in the context of genome reduction. Finally, knockout simulations in different metabolic systems reveal a gradual decrease in network robustness to different mutational events for bacterial endosymbionts at different stages of the symbiotic association. Conclusions: Stoichiometric analysis reveals few gene inactivation events whose effects on the functionality of S. glossinidius metabolic systems are drastic enough to account for the ecological transition from a free-living to hostdependent lifestyle. The decrease in network robustness across different metabolic systems may be associated with th